X-ray diffraction and theoretical approach to the molecular structure of (E)-2-(2-(1,3-dioxoisoindolin-2-yl)-1-(3-phenyl-3-methylcyclobutyl)ethylidene) hydrazine carboxamide

Article abstract of DOI:10.1007/s10870-012-0333-6

The title molecule (I), (E)-2-(2-(1,3-dioxoisoindolin- 2-yl)-1-(3-phenyl-3- methylcyclobutyl) ethylidene) hydrazine carboxamide (C₂₂H ₂₂N₄O₃), was synthesized and characterized by IR spectroscopy and single-cyrs

Full text of DOI:10.1007/s10870-012-0333-6

J Chem Crystallogr (2012) 42:897–904
DOI 10.1007/s10870-012-0333-6
ORIGINAL PAPER
X-Ray Diffraction and Theoretical Approach to the Molecular
Structure of (E)-2-(2-(1,3-dioxoisoindolin-2-yl)-1-(3-phenyl-3-
methylcyclobutyl)ethylidene) hydrazine carboxamide
Bet u¨ l Yılmaz
Ibrahim Yilmaz
•
Hanife Sara c¸ o g˘ lu
•
•
Nezihe C¸ alı s¸ kan
•
Alaaddin Cukurovali
Received: 15 August 2011 / Accepted: 6 June 2012 / Published online: 29 June 2012
Ó Springer Science+Business Media, LLC 2012
Abstract The title molecule (I), (E)-2-(2-(1,3-dioxoiso-
indolin-2-yl)-1-(3-phenyl-3-methylcyclobutyl) ethylidene)
hydrazine carboxamide (C H N O ), was synthesized
chemotherapeutic properties. Many compounds containing
the isoindolinone skeleton have shown antiviral, antileu-
kemic, antiinflammatory, antipsychotic and antiulcer
properties [1, 2]. Isoindolinones are useful for the synthesis
of various drugs and naturally occurring compounds [3, 4].
At the same time, it has been found that some isoindole-
1,3-dione derivates have protein kinase CK2 (Casein
Kinase) activity [5]. It is also well known that Phthalimides
and N-substituted phthalimides are an important class of
compounds because of their interesting biological activities
[6]. Phthalimides have also served as starting materials and
intermediates for the syntheses of alkaloids [7] and phar-
macophores [8]. In addition, these compounds containing
cyclobutane and phthalimide functions appear to be suit-
able candidates for further chemical modifications and may
be pharmacologically active and useful ligands in coordi-
nation chemistry [9].
2
2 22 4 3
and characterized by IR spectroscopy and single-cyrstal
X-ray diffraction. The compound cyrstallizes in the tri-
clinic space group P-1. In addition, the molecular geom-
etry, vibrational frequencies and frontier molecular orbitals
analysis of the title compound in the ground state have
been calculated by using the HF/6-31G(d) and B3LYP/6-
3
1G(d) methods. Molecular electrostatic potential of the
compound was also performed by the theoretical method.
Keywords X-ray structure determination Á DFT and HF
calculation Á B3LYP Á IR spectrum
Introduction
In this study, we report the characterization of (I) by using
single crystal X-ray. In addition we also have determined the
molecular geometry, vibrational spectra, and frontier
molecular orbital properties of this compound by using
density functional theory (DFT) the Hartree–Fock (HF) [10],
density functional using Becke’s three-parameter hybrid
functional [11] with the Lee, Yang, and Parr correlation
functional methods (B3LYP) [12]. Therefore, we compare
theoretical calculations and X-ray experimental data.
Isoindolinones and their derivatives have been investi-
gated widely due to their profound physiological and
B. Yılmaz (&) Á N. C¸ alı s¸ kan
Department of Physics, Faculty of Arts and Sciences, Ondokuz
Mayis University, 55139 Kurupelit, Samsun, Turkey
e-mail: betulylmaz84@gmail.com
H. Sara c¸ o g˘ lu
Department of Middle Education, Educational Faculty, Ondokuz
Mayis University, 55139 Kurupelit, Samsun, Turkey
Results and Discussion
I. Yilmaz
Department of Chemistry, Faculty of Science, Karamanoglu
Mehmetbey University, 71100 Karaman, Turkey
X-Ray Crystallography
The data collection was performed at 293 K on a Stoe-IPDS-2
diffractometer equipped with a graphite monochromated Mo
A. Cukurovali
Department of Chemistry, Faculty of Science, Firat University,
˚
2
3119 Elazig, Turkey
Ka radiation (k = 0.71073 A) [13]. The structure was solved
123

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J Chem Crystallogr (2012) 42:897–904
Table 1 Crystallographic data for compound (I)
Formula
22 22 4 3
C H N O
Molecular weight
Temperature (K)
390.44
293
˚
Wavelength (A)
0.71073
Triclinic
P-1
Crystal system
Space group
˚
Unit cell dimensions (A, °)
a
5.7444(4)
11.7325(8)
b
c
15.6240(12)
76.688(6)
85.672(6)
79.995(6)
1008.43(13)
2
a
b
c
Volume
Z
Fig. 1 The molecule of compound (I) showing the atom labelling
scheme
-3
)
Calculated density (g cm
1.286
T
min, Tmaks
0.9595, 0.9974
0.09
-
1
)
hydrogen atoms were included using a riding model and
˚
refined isotropically with C–H = 0.93–0.97 A and N–H =
l (mm
h
max (°)
26.5
˚
.86 A. U (H) = 1.2U (C, N), U (H) = 1.5U (for
0
Index ranges
h = -7 ? 6, k = -14 ? 14,
l = -19 ? 19
iso
eq
iso
eq
methyl group). Details of the data collection, cyrstal param-
eters and refinements are given in Table 1.
Reflections collected
8,686
4.141
1.684
0.94
Independent reflections
Observed reflections (I [ 2r)
Computational Method
S
R (I [ 2r)
wR (I [ 2r)
0.065
0.113
DFT calculations are carried out with Gaussian 03 program
[
17]. B3LYP hybrid method which uses Becke’s three
parameter exchange functional gradient corrected func-
tional. Lee et al. was used to predict the minimum energy
molecular geometry of the title compound. The molecular
structure of (I) in the ground state (in vacuo) was optimized
by DFT(B3LYP) [18] with the 6-31G(d) [19] and HF
direct methods using SHELXS-97 [14], and refined by a full-
matrix least-squares procedure using the program SHELXL-
9
7 [15], molecular graphics ORTEP-3 for Windows [16]. All
Fig. 2 A partial packing
diagram of the title
compound (I)
1
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J Chem Crystallogr (2012) 42:897–904
899
Table 2 Hydrogen bonding geometries for (I)
˚
D–H(A)
HÁÁÁA( A˚ )
DÁÁÁA( A˚ )
D–HÁÁÁA
D–HÁÁÁA(°)
i
N2–H2ÁÁÁO3
0.86
0.98
0.96
2.06
2.47
2.901(3)
3.202(4)
3.869(6)
167
132
i
C12–H12ÁÁÁO3
C8–O2ÁÁÁCg(2)
ii
3.339(4)
106.8(3)
Symmetry code: (i) -x ? 1, -y ? 1, -z ? 1, (ii) 1 - x, 1 - y, -z
Table 3 Selected theoretical and experimental geometric parameters
in the title compound
Parameters
Experimental
HF/
-31G(d)
B3LYP/
6-31G(d)
6
˚
Bond lengths (A)
O1–C1
1.215(6)
1.214(7)
1.225(4)
1.382(3)
1.272(4)
1.357(4)
1.383(6)
1.385(6)
1.487(7)
1.374(9)
1.471(8)
1.549(5)
1.552(5)
1.188
1.188
1.206
1.360
1.256
1.378
1.387
1.386
1.492
1.381
1.492
1.554
1.554
1.214
1.214
1.223
1.363
1.284
1.400
1.405
1.404
1.494
1.397
1.493
1.567
1.565
O2–C8
O3–C11
N1–N2
N1–C10
N2–C11
N4–C1
N4–C8
C1–C2
C2–C7
Fig. 3 Atom-by-atom superimposition of the structures calculated
(
(
red) [a HF/6-31G(d), b B3LYP/6-31G(d)], on the X-ray structure
black) for the title compound. Hydrogen atoms have been omitted for
C7–C8
C12–C13
clarity (Color figure online)
C14–C15
Bond angles (°)
N2–N1–C10
C1–N4–C9
C1–C2–C7
N2–C11–N3
C8–N4–C9
O1–C1–N4
O3–C11–N3
Torsion angles (°)
C10–N1–N2–C11
C2–C1–N4–C9
C9–C10–N1–N2
N4–C9–C10–C12
O1–C1–C2–C7
N1–C10–C12–C15
formula structure with the, C H N O , (I) shown in
2
2 22 4 3
117.7(2)
123.3(3)
108.5(5)
116.4(3)
124.1(4)
125.0(4)
122.5(3)
119.4
123.3
108.1
115.8
123.3
125.6
124.2
119.2
123.5
108.3
114.6
123.6
125.3
125.3
Fig. 1. The title molecule is composed of isoindolinone
group, phenyl, semicarbazone and cyclobutane moieties.
The molecule adopts E geometry about azomethine C=N
double bond. The N2–N1=C10–C12 torsion angle being
-1.8(5)° and N2–N1=C10–C9 torsion angle being –179.2°.
In addition, the moiety of C10–N1–N2–C11–O3–N3 atoms
˚
is nearly planar, with a mean deviation of -0.085 A for
atom N1. The cyclobutane ring is puckered and the C13/
C14/C15 plane forms a dihedral angle of 18.6° with the
C15/C12/C13 plane. This value is smaller than those,
which literature values for the puckering of the cyclobutane
ring are 26.8 (2)° [20], 23.5° [21] and 19.26 (17)° [22]. The
170.2(3)
-177.3(3)
-179.2
174.4
172.4
179.7
177.4
179.5
176.7
174.9
173.7
-179.9
177.2
176.8(3)
177.0(5)
176.9(3)
isoindoline ring is nearly planar, with a mean deviation of
˚
-179.9
177.7
0.047 A for atom N4. The two carbonyl, C1=O1 and
˚
C8=O2 bonds are almost same lengths with 1.214(6) A and
˚
.213(7) A, respectively. Similar value has been reported
1
methods. The ground state geometries were obtained in the
gas phase by full geometry optimization, starting from the
structural data.
˚
previously 1.204(3) A [23]. Hydrogen bonding interactions
of compound (I) will be seen in Fig. 2.
In the crystal packing, the molecules are linked to one
another with N–HÁÁÁO and C–HÁÁÁO hydrogen bonding. In
N–HÁÁÁO hydrogen bonding, the atom N2 at (x, y, z) acts as
a donor, via atom H2, to atom O3 at (-x ? 1, -y ? 1,
-z ? 1) . Resulting in the formation of N–HÁÁÁO mutual
hydrogen bonds which link two molecules related by an
Description of the Crystal Structure
The compound (I) crystallizes in the triclinic space group
P-1 with two molecules in the unit cell. The crystal
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9
00
J Chem Crystallogr (2012) 42:897–904
Fig. 4 Correlation of calculated
and experimental bond lengths
(
a), bond angles (b)
8
7
6
5
4
3
0
0
0
0
0
0
%
T
1
714
1693
4
000
3500
3000
2500
2000
1500
1000
500
Wavenumbers, nm
Fig. 5 The experimental FT-IR spectra of the title compound (1)
inversion centre. This configuration is characterized by an
2
hydrogen bonding. In addition, variations in O2=C8,
C8–N4, N4–C1, C1–C2, C2=C7 and C7–C8 bond lengths
(Table 3) confirm electron delocalization along the
–O2=C8–N4–C1–C2=C7–C8– segment when compared
with literature values for the isoindoline ring [23]. Then it
can be said this electron delocalization may cause inter-
molecular interaction, namely, C8–O2ÁÁÁCg(2) [Cg(2) is
2
R (8) graph set [24]. R (8) rings formed by hydrogen
2
2
bonds are centred at (1/2 ? n, 1/2 ? m, 1/2) (n, m, are
integer). On the other hand, atom C12 of cyclobutane ring
behaves as a donor, via atom H12, to atom O3 in C–HÁÁÁO
intermolecular hydrogen bonds around inversion centres.
Therefore, these hydrogen bonds generate bifurcated
1
23

J Chem Crystallogr (2012) 42:897–904
901
Table 4 Comparison of the observed and calculated vibrational
spectra of the title compound
S(5) graph set [24], details of these bonds and interaction
are given in Table 2.
Assignments
Experimental HF/6-
-
B3LYP/6-
31G(d) (cm
1
)
-1
-1
(cm
31G(d) (cm
)
)
DFT and HF Calculations
m
as(NH
2
)
3535
3416
3186
3087
2925
2858
1768
1714
1693
1550
1425
3561
3445
3457
3040
3024
2912
1843
1786
1763
1734
1463
1189
3581
3457
3431
3098
3085
2948
1738
1737
1760
1645
1423
1217
The optimized structure parameters of the structure
m
s
(NH )
2
(
I) calculated by DFT (B3LYP) and HF level with the
-31G(d) basis set are listed in Table 3. As seen from
m(NH)
6
m
m
m
m
m
s
s
s
s
(CH) iso.
Table 3, most of the optimized bond lengths are slightly
longer than the experimental values and the bond angles
are slightly different from the experimental ones. Because,
the molecular states are different during experimental and
theoretical processes. One isolated molecule is considered
in gas phase in theoretical calculation, whereas many
packed molecules are treated in solid phase during the
experimental measurement. When the X-ray structure
of (I) is compared with HF/6-31G(d) and B3LYP/6-
31G(d) optimized counterpart (see Fig. 3), it can be easily
seen that they are slightly different each other. The RMS fit
of the atomic position of (I) to those of its HF and B3LYP
(CH) aromatic
(CH
2
)
(C=O)
as(C=O)
m(C=O)
m(C=N)
b(NH)
2
x(CH ) ? b(CH) 1251
Vibrational modes: m, stretching; b, bending; x, wagging; s, sym-
metric; as, asymmetric; iso, isoindolinone ring
˚
optimized counterparts are 0.3012 and 0.2766 A, respec-
tively. Consequently, the B3LYP method correlates well
for the geometrical parameters when compared with HF.
Owing to our calculations, HF and B3LYP methods
correlate well for the bond length comparison. The largest
differences between experimental and calculated bond
˚
˚
lengths about 0.0238 A for HF and 0.04258 A for B3LYP.
The bond angles provided by HF method is the closest to
the experimental values (see Table 3). The largest differ-
ence is about 1.797° in the case of HF method, while this
difference is 2.828° for B3LYP method. The same trend
was also observed in torsion angles. The largest differences
are 4.673° and 4.937° for B3LYP and HF methods,
respectively. Although there are some differences between
the theoretical and the experimental values, the optimized
structural parameters can well reproduce the experimental
ones and they are basis for the discussions hereafter. The
correlation between the experimental and calculated geo-
metric parameters is given in Fig. 4.
Infrared Spectra
Harmonic vibrational frequencies of (I) were calculated by
using B3LYP and HF method with 6-31G(d) basis set and
the obtained frequencies were scaled by 0.9613 and 0.8929
[
25], respectively. The FT-IR spectra of (I) is shown in
Fig. 6 Correlation graphics of calculated and experimental frequen-
cies of the title compound. a HF and b DFT
Fig. 5. The formation of hydrogen bonds causes the sig-
nificant low-wavelength shift and broadening of N–H
stretching mode, and it can be observed around
-
1
N4/C1/C2/C7/C8]. The distance between O2 and the
˚
centroid Cg2 at (1 - x, 1 - y, -z) is 3.339(4) A and
2500–3500 cm with multiple peaks [26]. In this study,
1
-
the N2–H stretching mode is observed at 3186 cm . On
the other hand, N2–H bending mode is observed at
C8–O2ÁÁÁCg2 angle is 106.8(3)°. Beside of these, intra-
molecular N3–HÁÁÁN1 hydrogen bond bring into existence
-
1425 cm . This value is given with 1499 cm [27] in
1
-1
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J Chem Crystallogr (2012) 42:897–904
Fig. 7 Molecular electrostatic
potential map calculated at
B3LYP/6-31G(d) level (Color
figure online)
stretching vibration can be explained by the existence of
the C12–H12ÁÁÁO3 intermolecular hydrogen bond given in
Table 2, because isolated molecules are taken into con-
sideration in calculations [29]. Experimental frequencies of
(
I) were compared with calculated vibrational frequencies
by correlation graphics given in Fig. 6. The correlation
graphics in Fig. 6 show that experimental fundamentals are
found to have a good correlation with calculations by
B3LYP method when compared to HF method.
Molecular Electrostatic Potential
Molecular electrostatic potential maps provide the isosur-
face values with the location of negative and positive elec-
trostatic potentials. The differences between nucleophilicity
and electrophilicity may affect its the proton donating or
accepting ability of the compound [30]. While the negative
electrostatic potential corresponds to an attraction of the
proton by the concentrated electron density in the molecule
(and is colored in shades of red on the EPS surface), the
positive electrostatic potential corresponds to repulsion of
the proton by atomic nuclei in regions where low electron
density exists and the nuclear charge is incompletely shiel-
ded (and is colored in shades of blue) [31].
Fig. 8 HOMO and LUMO of the title compound
the literature. As can be seen in Table 4 due to N2–H2ÁÁÁO3
intermolecular hydrogen bonding, experimental m(N–H)
bending vibration increases while m(N–H) stretching
vibration decreases [28]. The strong and broad band cen-
Figure 7 shows the molecular electrostatic potential
(MEP), was determined using B3LYP/6-31G(d) method.
The different values of the electrostatic potential at the
surface are represented by different colors. As can be seen
in Fig. 7, the negative (red) region is localized on the un-
protonated atom of, O3, with a minimum value of -0.0632
a.u. However, maximum positive (blue) region is localized
on atoms C12 and N2 probably due to the hydrogen, with a
maximum value of 0.0632 a.u. and green represents
regions of zero potential. Therefore, Fig. 7 confirms the
-
1
tered between 3096 and 2922 cm
are attributed to
asymmetric and symmetric C–H stretching vibrations of
aromatic and aliphatic groups. m(C=O) vibrations are
observed at 1771, 1726 and 1677 cm in the infrared
-
1
experimental spectra, while the calculated values are 1843,
-1
-
786 and 1763 cm for HF, 1783, 1737 and 1760 cm
1
1
for B3LYP, respectively. This difference given for C=O
1
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J Chem Crystallogr (2012) 42:897–904
903
NH2
C
NH2
C
O
O
NH
O
NH
O
N
C
O
H2N
C
CH2 Cl
+
HN
CH2
N
H C
3
H C
3
O
O
Scheme 1 Synthesis scheme of the title compound (I)
existence of an intermolecular N–HÁÁÁO and C–HÁÁÁO
interactions. In addition, the weak red regions associated
with O1 and O2 atoms with a value of -0.043 a.u. And
also the carbonyl oxygen atom, O2, is involved in inter-
molecular C8–O2ÁÁÁCg(2) interaction. Therefore it can be
said these sites give the information about the region from
where the compound can have intermolecular interactions.
m(aliphatics), 1768 and 1714 m(C=O), 1693 (C=O),
-
1
1
1550 cm m(C=N). Characteristic H NMR shifts (DMSO-
d , d, ppm): 1.49 (s, 3H, –CH on cyclobutane), 2.31–2.52
(m, 4H, –CH –, in cyclobutane ring), 3.84 (quint,
6
3
2
j = 7.8 Hz, 1H, [CH– in cyclobutane ring), 4.38 (s, 2H,
–CH –N), 5.77 (brs, 2H, –NH ), 7.12–7.21 (m, 3H, aro-
2
2
matics), 7.26–7.37 (m, 2H, aromatics), 7.80–7.96 (m, 4H,
1
aromatics), 9.26 (s, 1H, –NH). Characteristic C NMR
3
Frontier Molecular Orbitals Analysis
shifts (DMSO-d , d, ppm): 169.35, 158.45, 153.30, 147.83,
6
136.39, 133.33, 130.04, 127.18, 126.15, 124.93, 41.21,
Figure 8 shows the distributions and energy levels of
38.62, 33.82, 31.02, 29.26 (Scheme 1).
HOMO and LUMO orbitals of (I) by obtained at the B3LYP/
6
-31G(d) method. The calculations indicate that the title
compound has 103 occupied molecular orbitals. While
highest occupied molecular orbitals (HOMOs) localized on
the semicarbazone moiety, lowest unoccupied molecular
orbitals (LUMOs) are localized on the isoindoline ring.
Because of that HOMO and LUMO are mainly localized on
different parts of the title molecule, they are mostly the
p-antibonding type orbitals. The value of the energy seper-
ation between the HOMO and LUMO is 3.973 eV.
Conclusions
(E)-2-(2-(1,3-dioxoisoindolin-2-yl)-1-(3-phenyl-3-methyl
cyclobutyl)ethylidene) hydrazine carboxamide has been
synthesized and characterized by IR and X-ray single-
crystal diffraction. The X-ray structure is found to be very
slightly different from its optimized counterparts and the
crystal structure is stabilized by N–HÁÁÁO and C–HÁÁÁO type
hydrogen bonds. The theoretical calculations performed by
HF and DFT (B3LYP) support the solid state structure.
According to observed results, B3LYP method shows a
better fit to experimental values than HF in evaluating
geometrical parameters. It is noted here that the experi-
mental results are for the solid phase and the theoretical
calculations are for the gaseous phase. In the solid state, the
existence of the crystal field together with the intermolecular
interactions holds the molecules together, which results in
differences between the calculated and experimental values
for the bond parameters. The MEP map shows that the
negative potential sites are on oxygen atoms as well as the
positive potential sites are around the hydrogen atoms and so
MEP map confirms the existence of intermolecular N–HÁÁÁO
and C–HÁÁÁO interactions. Therefore, all the calculated
spectra, bond lengths and angles of this structure are in good
agreement with the experimental data.
Experimental
Synthesis of the Title Compound
To a solution of phthalimide (1.4713 g, 10 mmol) in 50 mL
of ethanol, 1-methyl-1-phenyl-3-(2-chloro-1-oxoethyl)
cyclobutane (2.2271 g, 10 mmol) in 20 mL of absolute
ethanol was added dropwise. End of the reaction was
determined by monitoring the course of the reaction with IR
spectroscopy. Subsequently, a solution of thiosemicarbazide
(
0.9113 g, 10 mmol) in 20 mL of absolute ethanol was
added. After addition of thiosemicarbazide, the temperature
was raised to 323–328 K and stirred at this temperature for
2
h. The solution was cooled to room temperature and then
made alkaline with an aqueous solution of NH (5%), and
3
white precipitate separated by suction. washed with aqueous
NH solution several times and dried in air. Suitable single
3
crystals for crystal structure determination were obtained by
slow evaporation of its ethanol solution. Yield: 89%, melt-
ing point: 523 K. Characteristic IR bands: 35,345 and
Supplementary Material
Crystallographic data for the structure analysis have been
deposited with the Cambridge Crystallographic Data Centre,
-
1
-1
3
,416 cm m(–NH ), 3,186 cm m(–NH–), 2,967–2858
2
123

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J Chem Crystallogr (2012) 42:897–904
CCDC No 838406 Copies of this information may be
obtained free of charge from the Director, CCDC, 12 Union
Road, Cambridge CB2 1EZ, UK (fax: ?44-1223-336033;
e-mail: deposit@ccdc.cam.ac.uk or www: http://www.cede.
cam.ac.uk).
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maromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY,
Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen
W, Wong MW, Gonzalez C, Pople JA (2004) Gaussian 03,
revision D.01. Gaussian, Inc., Wallingford
Acknowledgments The authors wish to acknowledge the Faculty of
Arts and Sciences, Ondokuz Mayis University, Turkey, for the use of
the STOE IPDS-II diffractometer (purchased under grant F.279 of the
University Research Fund).
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